Biowulf High Performance Computing at the NIH
Neuroconstruct on Biowulf

Neuroconstruct is an application for developing 3D networks for biologically realistic neuronal simulations. Those networks can incorporate dendritic morphologies and realistic cell membrane conductances. Neuroconstruct is implemented in Java and generates script files for the following neuronal simulation applications: NEURON, GENESIS, MOOSE, PSICS and PyNN.


Important Notes

Interactive jobs should be used for debugging, graphics, or applications that cannot be run as batch jobs.

Allocate an interactive session and run the program.
Sample session (user input in bold):

[user@biowulf]$ sinteractive
salloc.exe: Pending job allocation 46116226
salloc.exe: job 46116226 queued and waiting for resources
salloc.exe: job 46116226 has been allocated resources
salloc.exe: Granted job allocation 46116226
salloc.exe: Waiting for resource configuration
salloc.exe: Nodes cn3144 are ready for job
[user@cn3144 ~]$ module load neuroconstruct
[+] Loading neuroconstruct  1.7.2 
[user@cn3144 ~]$ neuroconstruct &
[user@cn3144 ~]$ Running neuroConstruct from: /usr/local/apps/neuroconstruct/1.7.2 with max Java heap size of 450M

neuroConstruct v1.7.1 starting...
To start application with extra memory, see in the neuroConstruct home directory.

neuroconstruct GUI window

Export your network to a Neuron simulation script

In order to run simulations on Neuroconstruct using Biowulf's Neuron, the path to the neuron executable and the command line terminal must be set up as follows:

1. Click on Settings -> General Properties & Project Defaults

neuroconstruct GUI window

2. You should now be able to see the General Preferences windows

neuroconstruct GUI window

3. Set NEURON home directory to /usr/local/apps/neuron/nrn-7.5/x86_64 and Command line to xterm as shown below:

neuroconstruct GUI window

4. Now click Save and you are set up to export your neuroconstruct network to a Neuron simulation script. Note that the simulation scripts are saved to the Default location projects directory, wihch you can also change in the General Preferences menu shown above. The Neuron simulation scripts can be executed on the command terminal outside neuroconstruct.